Comparative Genomic Analysis of Cosmopolitan Dominant Cyanobacteria Microcoleus vaginatus and Microcystis aeruginosa

Cyanobacteria inhabit ecosystems ranging from oligotrophic deserts to eutrophic lakes, yet it remains unclear whether distantly related species dominate in disparate habitats, share common genomic features, or show divergent specialization. Here, we established a comparative framework of Microcoleus vaginatus, the pioneer stabilizer of biocrusts, and Microcystis aeruginosa, a major cause of freshwater blooms worldwide. Our dataset comprises 504 high-quality cyanobacterial genomes, including 132 M. vaginatus, 148 M. aeruginosa, and 224 reference taxa, for analyses of genome architecture, functional repertoires, and genomic plasticity. Both focal lineages showed signatures of extensive horizontal gene transfer and shared a small set of conserved orthologous groups, annotated as FAD-dependent oxidoreductases, manganese efflux, and class II aldolases. Nevertheless, the two lineages followed distinct genomic strategies. M. vaginatus expands regulatory breadth and stress-resilience gene families, whereas M. aeruginosa shows evidence of genome streamlining and rapid nutrient exploitation. Notably, we hypothesize that aquatic M. vaginatus strains retain ancestral terrestrial genomic features while gradually acquiring potential aquatic-specific adaptations. Together, these results reveal a two-tier architecture associated with cyanobacterial dominance and provide a testable hypothesis for how cyanobacterial lineages may respond to global change pressures.